BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504635.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 344,664,866 number of mapped reads = 299,387,913 (86.86%) number of supplementary alignments = 3,257,577 (0.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 150,163,904 number of mapped paired reads (second in pair) = 149,224,009 number of mapped paired reads (both in pair) = 297,046,124 number of mapped paired reads (singletons) = 2,341,789 number of mapped bases = 29,551,948,728 bp number of sequenced bases = 29,544,889,579 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,084,441 duplication rate = 25.31% >>>>>>> Insert size mean insert size = 40,489.3474 std insert size = 1,925,209.0428 median insert size = 366 >>>>>>> Mapping quality mean mapping quality = 53.6311 >>>>>>> ACTG content number of A's = 7,417,955,630 bp (25.11%) number of C's = 7,231,693,883 bp (24.48%) number of T's = 7,456,379,582 bp (25.24%) number of G's = 7,402,853,043 bp (25.06%) number of N's = 36,007,441 bp (0.12%) GC percentage = 49.53% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 224,945,572 number of insertions = 2,207,702 mapped reads with insertion percentage = 0.72% number of deletions = 2,815,218 mapped reads with deletion percentage = 0.91% homopolymer indels = 39.07% >>>>>>> Coverage mean coverageData = 9.5461X std coverageData = 37.567X There is a 62.29% of reference with a coverageData >= 1X There is a 51.35% of reference with a coverageData >= 2X There is a 43.96% of reference with a coverageData >= 3X There is a 38.5% of reference with a coverageData >= 4X There is a 34.18% of reference with a coverageData >= 5X There is a 30.68% of reference with a coverageData >= 6X There is a 27.78% of reference with a coverageData >= 7X There is a 25.33% of reference with a coverageData >= 8X There is a 23.24% of reference with a coverageData >= 9X There is a 21.44% of reference with a coverageData >= 10X There is a 19.86% of reference with a coverageData >= 11X There is a 18.48% of reference with a coverageData >= 12X There is a 17.26% of reference with a coverageData >= 13X There is a 16.17% of reference with a coverageData >= 14X There is a 15.19% of reference with a coverageData >= 15X There is a 14.31% of reference with a coverageData >= 16X There is a 13.52% of reference with a coverageData >= 17X There is a 12.79% of reference with a coverageData >= 18X There is a 12.13% of reference with a coverageData >= 19X There is a 11.52% of reference with a coverageData >= 20X There is a 10.97% of reference with a coverageData >= 21X There is a 10.46% of reference with a coverageData >= 22X There is a 9.98% of reference with a coverageData >= 23X There is a 9.54% of reference with a coverageData >= 24X There is a 9.13% of reference with a coverageData >= 25X There is a 8.75% of reference with a coverageData >= 26X There is a 8.4% of reference with a coverageData >= 27X There is a 8.07% of reference with a coverageData >= 28X There is a 7.76% of reference with a coverageData >= 29X There is a 7.46% of reference with a coverageData >= 30X There is a 7.19% of reference with a coverageData >= 31X There is a 6.93% of reference with a coverageData >= 32X There is a 6.68% of reference with a coverageData >= 33X There is a 6.45% of reference with a coverageData >= 34X There is a 6.23% of reference with a coverageData >= 35X There is a 6.03% of reference with a coverageData >= 36X There is a 5.83% of reference with a coverageData >= 37X There is a 5.64% of reference with a coverageData >= 38X There is a 5.46% of reference with a coverageData >= 39X There is a 5.29% of reference with a coverageData >= 40X There is a 5.13% of reference with a coverageData >= 41X There is a 4.98% of reference with a coverageData >= 42X There is a 4.83% of reference with a coverageData >= 43X There is a 4.69% of reference with a coverageData >= 44X There is a 4.56% of reference with a coverageData >= 45X There is a 4.43% of reference with a coverageData >= 46X There is a 4.31% of reference with a coverageData >= 47X There is a 4.19% of reference with a coverageData >= 48X There is a 4.08% of reference with a coverageData >= 49X There is a 3.97% of reference with a coverageData >= 50X There is a 3.86% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2840392581 11.395729204622523 36.95451949970015 chr2 243199373 2397207193 9.85696288369954 28.914227811603737 chr3 198022430 1400261283 7.071225633379006 24.02938038482343 chr4 191154276 915099711 4.787231183884162 14.90576367241941 chr5 180915260 1988915384 10.993629746877074 31.177744707818448 chr6 171115067 851026579 4.973416975607414 18.23316807590113 chr7 159138663 2034769124 12.78613936828161 32.825959270381674 chr8 146364022 1571637012 10.73786433663322 28.150605272711875 chr9 141213431 1024131019 7.25236269487709 69.57774220334021 chr10 135534747 1199369222 8.849164133533964 28.195328222154178 chr11 135006516 1381316806 10.23148250118535 35.10592673169444 chr12 133851895 1245245990 9.30316294737553 27.713948476357437 chr13 115169878 136513355 1.1853216949661092 5.526683960329028 chr14 107349540 911611681 8.491994292663014 22.976153049170016 chr15 102531392 1076633262 10.50052321536803 29.51255991452921 chr16 90354753 1913333955 21.175797525560167 52.831339004157236 chr17 81195210 1278022020 15.740115950189672 41.311217340292586 chr18 78077248 507006112 6.493647317077569 70.99099431370283 chr19 59128983 1604398925 27.133883310660018 111.83208906685113 chr20 63025520 1009813742 16.022299252747143 48.45472953627048 chr21 48129895 316622907 6.578508160053123 21.31289794822031 chr22 51304566 740682112 14.436962823153012 35.55618649736308 chrMT 16571 2865132 172.90036811296844 66.54316023788819 chrX 155270560 1161345121 7.479493350188213 18.042005620839717 chrY 59373566 43728500 0.7364977875844614 32.65441517547935